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<div class="title">types.hpp</div>  </div>
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<div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno">    1</span>&#160;<span class="comment">/*</span></div>
<div class="line"><a name="l00002"></a><span class="lineno">    2</span>&#160;<span class="comment">* Copyright (c) 2019, NVIDIA CORPORATION.  All rights reserved.</span></div>
<div class="line"><a name="l00003"></a><span class="lineno">    3</span>&#160;<span class="comment">*</span></div>
<div class="line"><a name="l00004"></a><span class="lineno">    4</span>&#160;<span class="comment">* NVIDIA CORPORATION and its licensors retain all intellectual property</span></div>
<div class="line"><a name="l00005"></a><span class="lineno">    5</span>&#160;<span class="comment">* and proprietary rights in and to this software, related documentation</span></div>
<div class="line"><a name="l00006"></a><span class="lineno">    6</span>&#160;<span class="comment">* and any modifications thereto.  Any use, reproduction, disclosure or</span></div>
<div class="line"><a name="l00007"></a><span class="lineno">    7</span>&#160;<span class="comment">* distribution of this software and related documentation without an express</span></div>
<div class="line"><a name="l00008"></a><span class="lineno">    8</span>&#160;<span class="comment">* license agreement from NVIDIA CORPORATION is strictly prohibited.</span></div>
<div class="line"><a name="l00009"></a><span class="lineno">    9</span>&#160;<span class="comment">*/</span></div>
<div class="line"><a name="l00010"></a><span class="lineno">   10</span>&#160; </div>
<div class="line"><a name="l00011"></a><span class="lineno">   11</span>&#160;<span class="preprocessor">#pragma once</span></div>
<div class="line"><a name="l00012"></a><span class="lineno">   12</span>&#160; </div>
<div class="line"><a name="l00013"></a><span class="lineno">   13</span>&#160;<span class="preprocessor">#include &lt;cstdint&gt;</span></div>
<div class="line"><a name="l00014"></a><span class="lineno">   14</span>&#160;<span class="preprocessor">#include &lt;string&gt;</span></div>
<div class="line"><a name="l00015"></a><span class="lineno">   15</span>&#160; </div>
<div class="line"><a name="l00016"></a><span class="lineno">   16</span>&#160;<span class="keyword">namespace </span>claragenomics</div>
<div class="line"><a name="l00017"></a><span class="lineno">   17</span>&#160;{</div>
<div class="line"><a name="l00018"></a><span class="lineno">   18</span>&#160; </div>
<div class="line"><a name="l00019"></a><span class="lineno">   19</span>&#160;<span class="keyword">namespace </span>cudamapper</div>
<div class="line"><a name="l00020"></a><span class="lineno">   20</span>&#160;{</div>
<div class="line"><a name="l00021"></a><span class="lineno">   21</span>&#160; </div>
<div class="line"><a name="l00025"></a><span class="lineno"><a class="line" href="structclaragenomics_1_1cudamapper_1_1ArrayBlock.html">   25</a></span>&#160;<span class="keyword">struct </span><a class="code" href="structclaragenomics_1_1cudamapper_1_1ArrayBlock.html">ArrayBlock</a></div>
<div class="line"><a name="l00026"></a><span class="lineno">   26</span>&#160;{</div>
<div class="line"><a name="l00028"></a><span class="lineno"><a class="line" href="structclaragenomics_1_1cudamapper_1_1ArrayBlock.html#a3fca81e893b35e0648977b00f21b7e7e">   28</a></span>&#160;    <span class="keywordtype">size_t</span> <a class="code" href="structclaragenomics_1_1cudamapper_1_1ArrayBlock.html#a3fca81e893b35e0648977b00f21b7e7e">first_element_</a>;</div>
<div class="line"><a name="l00030"></a><span class="lineno"><a class="line" href="structclaragenomics_1_1cudamapper_1_1ArrayBlock.html#a33ff27afee2ddb07e6fbdda0ff1de229">   30</a></span>&#160;    std::uint32_t <a class="code" href="structclaragenomics_1_1cudamapper_1_1ArrayBlock.html#a33ff27afee2ddb07e6fbdda0ff1de229">block_size_</a>;</div>
<div class="line"><a name="l00031"></a><span class="lineno">   31</span>&#160;};</div>
<div class="line"><a name="l00032"></a><span class="lineno">   32</span>&#160; </div>
<div class="line"><a name="l00034"></a><span class="lineno">   34</span>&#160;<span class="keyword">using</span> position_in_read_t = std::uint32_t;</div>
<div class="line"><a name="l00036"></a><span class="lineno">   36</span>&#160;<span class="keyword">using</span> representation_t = std::uint64_t; <span class="comment">// this depends on kmer size, in some cases could also be 32-bit</span></div>
<div class="line"><a name="l00038"></a><span class="lineno">   38</span>&#160;<span class="comment"></span><span class="keyword">using</span> read_id_t = std::uint64_t; <span class="comment">// can this be 32-bit?</span></div>
<div class="line"><a name="l00039"></a><span class="lineno">   39</span>&#160; </div>
<div class="line"><a name="l00042"></a><span class="lineno">   42</span>&#160;<span class="keyword">enum class</span> RelativeStrand : unsigned char</div>
<div class="line"><a name="l00043"></a><span class="lineno">   43</span>&#160;{</div>
<div class="line"><a name="l00044"></a><span class="lineno">   44</span>&#160;    Forward = <span class="charliteral">&#39;+&#39;</span>,</div>
<div class="line"><a name="l00045"></a><span class="lineno">   45</span>&#160;    Reverse = <span class="charliteral">&#39;-&#39;</span>,</div>
<div class="line"><a name="l00046"></a><span class="lineno">   46</span>&#160;};</div>
<div class="line"><a name="l00047"></a><span class="lineno">   47</span>&#160; </div>
<div class="line"><a name="l00051"></a><span class="lineno"><a class="line" href="structclaragenomics_1_1cudamapper_1_1Anchor.html">   51</a></span>&#160;<span class="keyword">struct </span><a class="code" href="structclaragenomics_1_1cudamapper_1_1Anchor.html">Anchor</a></div>
<div class="line"><a name="l00052"></a><span class="lineno">   52</span>&#160;{</div>
<div class="line"><a name="l00054"></a><span class="lineno">   54</span>&#160;<span class="preprocessor">#ifdef __CUDACC__</span></div>
<div class="line"><a name="l00055"></a><span class="lineno">   55</span>&#160;    __host__ __device__ <a class="code" href="structclaragenomics_1_1cudamapper_1_1Anchor.html#af4dc10f114030a8e3a53f3bad3cd20b2">Anchor</a>()</div>
<div class="line"><a name="l00056"></a><span class="lineno">   56</span>&#160;    {</div>
<div class="line"><a name="l00057"></a><span class="lineno">   57</span>&#160;    }</div>
<div class="line"><a name="l00058"></a><span class="lineno">   58</span>&#160;<span class="preprocessor">#else</span></div>
<div class="line"><a name="l00059"></a><span class="lineno"><a class="line" href="structclaragenomics_1_1cudamapper_1_1Anchor.html#af4dc10f114030a8e3a53f3bad3cd20b2">   59</a></span>&#160;    <a class="code" href="structclaragenomics_1_1cudamapper_1_1Anchor.html#af4dc10f114030a8e3a53f3bad3cd20b2">Anchor</a>()</div>
<div class="line"><a name="l00060"></a><span class="lineno">   60</span>&#160;    {</div>
<div class="line"><a name="l00061"></a><span class="lineno">   61</span>&#160;    }</div>
<div class="line"><a name="l00062"></a><span class="lineno">   62</span>&#160;<span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00063"></a><span class="lineno">   63</span>&#160;    read_id_t <a class="code" href="structclaragenomics_1_1cudamapper_1_1Anchor.html#a3c79e476eae0672a9a941e0980b6dcc3">query_read_id_</a>;</div>
<div class="line"><a name="l00066"></a><span class="lineno"><a class="line" href="structclaragenomics_1_1cudamapper_1_1Anchor.html#ae9ae1af9e2feaea69ebde6b165966cec">   66</a></span>&#160;    read_id_t <a class="code" href="structclaragenomics_1_1cudamapper_1_1Anchor.html#ae9ae1af9e2feaea69ebde6b165966cec">target_read_id_</a>;</div>
<div class="line"><a name="l00068"></a><span class="lineno"><a class="line" href="structclaragenomics_1_1cudamapper_1_1Anchor.html#ad5e41665c86c77044b2ba2c939fdbb86">   68</a></span>&#160;    position_in_read_t <a class="code" href="structclaragenomics_1_1cudamapper_1_1Anchor.html#ad5e41665c86c77044b2ba2c939fdbb86">query_position_in_read_</a>;</div>
<div class="line"><a name="l00070"></a><span class="lineno"><a class="line" href="structclaragenomics_1_1cudamapper_1_1Anchor.html#ad58b2a619bd71c37c337ed44e45b4d23">   70</a></span>&#160;    position_in_read_t <a class="code" href="structclaragenomics_1_1cudamapper_1_1Anchor.html#ad58b2a619bd71c37c337ed44e45b4d23">target_position_in_read_</a>;</div>
<div class="line"><a name="l00071"></a><span class="lineno">   71</span>&#160;};</div>
<div class="line"><a name="l00072"></a><span class="lineno">   72</span>&#160; </div>
<div class="line"><a name="l00077"></a><span class="lineno"><a class="line" href="structclaragenomics_1_1cudamapper_1_1Overlap.html">   77</a></span>&#160;<span class="keyword">typedef</span> <span class="keyword">struct </span><a class="code" href="structclaragenomics_1_1cudamapper_1_1Overlap.html">Overlap</a></div>
<div class="line"><a name="l00078"></a><span class="lineno">   78</span>&#160;{</div>
<div class="line"><a name="l00080"></a><span class="lineno"><a class="line" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#a3d98a09e4ccd8bda66cb09a72adaf1fc">   80</a></span>&#160;    read_id_t <a class="code" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#a3d98a09e4ccd8bda66cb09a72adaf1fc">query_read_id_</a>;</div>
<div class="line"><a name="l00082"></a><span class="lineno"><a class="line" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#a6d01fc190b1cba1c6b41cd89d672b032">   82</a></span>&#160;    read_id_t <a class="code" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#a6d01fc190b1cba1c6b41cd89d672b032">target_read_id_</a>;</div>
<div class="line"><a name="l00084"></a><span class="lineno"><a class="line" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#aef98d06e839295136d197fee76feb95e">   84</a></span>&#160;    position_in_read_t <a class="code" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#aef98d06e839295136d197fee76feb95e">query_start_position_in_read_</a>;</div>
<div class="line"><a name="l00086"></a><span class="lineno"><a class="line" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#a03cb25f83ca6344ad1b4108c1d910f0c">   86</a></span>&#160;    position_in_read_t <a class="code" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#a03cb25f83ca6344ad1b4108c1d910f0c">target_start_position_in_read_</a>;</div>
<div class="line"><a name="l00088"></a><span class="lineno"><a class="line" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#a20866810acf35523e87efcb66181a224">   88</a></span>&#160;    position_in_read_t <a class="code" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#a20866810acf35523e87efcb66181a224">query_end_position_in_read_</a>;</div>
<div class="line"><a name="l00090"></a><span class="lineno"><a class="line" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#ad4721b3555a83acb588c54dc369f7797">   90</a></span>&#160;    position_in_read_t <a class="code" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#ad4721b3555a83acb588c54dc369f7797">target_end_position_in_read_</a>;</div>
<div class="line"><a name="l00092"></a><span class="lineno"><a class="line" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#a7d37018aff3304bbe75b2d612b55c057">   92</a></span>&#160;    <span class="keywordtype">char</span>* <a class="code" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#a7d37018aff3304bbe75b2d612b55c057">query_read_name_</a> = 0;</div>
<div class="line"><a name="l00094"></a><span class="lineno"><a class="line" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#afcb7e39abf2761899ff1abb3c95b82ca">   94</a></span>&#160;    <span class="keywordtype">char</span>* <a class="code" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#afcb7e39abf2761899ff1abb3c95b82ca">target_read_name_</a> = 0;</div>
<div class="line"><a name="l00096"></a><span class="lineno"><a class="line" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#a1c0b9bac9b2e15f70c60fcdae9728fd7">   96</a></span>&#160;    RelativeStrand <a class="code" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#a1c0b9bac9b2e15f70c60fcdae9728fd7">relative_strand</a>;</div>
<div class="line"><a name="l00098"></a><span class="lineno"><a class="line" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#ab3594748a49ae4472ca28a03b05ddb7d">   98</a></span>&#160;    std::uint32_t <a class="code" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#ab3594748a49ae4472ca28a03b05ddb7d">num_residues_</a> = 0;</div>
<div class="line"><a name="l00100"></a><span class="lineno"><a class="line" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#a7677cc8d0aa20fc788b57f85905e051b">  100</a></span>&#160;    std::uint32_t <a class="code" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#a7677cc8d0aa20fc788b57f85905e051b">query_length_</a> = 0;</div>
<div class="line"><a name="l00102"></a><span class="lineno"><a class="line" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#a2da1b559c8e45c6bc48eda8b60e40c11">  102</a></span>&#160;    std::uint32_t <a class="code" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#a2da1b559c8e45c6bc48eda8b60e40c11">target_length_</a> = 0;</div>
<div class="line"><a name="l00104"></a><span class="lineno"><a class="line" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#a31d4f58b24a2e3fc57b5bca803827360">  104</a></span>&#160;    <span class="keywordtype">bool</span> <a class="code" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#a31d4f58b24a2e3fc57b5bca803827360">overlap_complete</a> = <span class="keyword">false</span>;</div>
<div class="line"><a name="l00106"></a><span class="lineno"><a class="line" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#ad9b3ed3f91b4979afb6198cea2d77e54">  106</a></span>&#160;    <span class="keywordtype">char</span>* <a class="code" href="structclaragenomics_1_1cudamapper_1_1Overlap.html#ad9b3ed3f91b4979afb6198cea2d77e54">cigar_</a> = 0;</div>
<div class="line"><a name="l00107"></a><span class="lineno">  107</span>&#160;} <a class="code" href="structclaragenomics_1_1cudamapper_1_1Overlap.html">Overlap</a>;</div>
<div class="line"><a name="l00108"></a><span class="lineno">  108</span>&#160; </div>
<div class="line"><a name="l00109"></a><span class="lineno">  109</span>&#160;} <span class="comment">// namespace cudamapper</span></div>
<div class="line"><a name="l00110"></a><span class="lineno">  110</span>&#160; </div>
<div class="line"><a name="l00111"></a><span class="lineno">  111</span>&#160;} <span class="comment">// namespace claragenomics</span></div>
</div><!-- fragment --></div><!-- contents -->
<div class="ttc" id="astructclaragenomics_1_1cudamapper_1_1Overlap_html_a7677cc8d0aa20fc788b57f85905e051b"><div class="ttname"><a href="structclaragenomics_1_1cudamapper_1_1Overlap.html#a7677cc8d0aa20fc788b57f85905e051b">claragenomics::cudamapper::Overlap::query_length_</a></div><div class="ttdeci">std::uint32_t query_length_</div><div class="ttdoc">Length of query sequence.</div><div class="ttdef"><b>Definition:</b> types.hpp:100</div></div>
<div class="ttc" id="astructclaragenomics_1_1cudamapper_1_1Overlap_html_ad9b3ed3f91b4979afb6198cea2d77e54"><div class="ttname"><a href="structclaragenomics_1_1cudamapper_1_1Overlap.html#ad9b3ed3f91b4979afb6198cea2d77e54">claragenomics::cudamapper::Overlap::cigar_</a></div><div class="ttdeci">char * cigar_</div><div class="ttdoc">CIGAR string for alignment of mapped section.</div><div class="ttdef"><b>Definition:</b> types.hpp:106</div></div>
<div class="ttc" id="astructclaragenomics_1_1cudamapper_1_1Overlap_html_ab3594748a49ae4472ca28a03b05ddb7d"><div class="ttname"><a href="structclaragenomics_1_1cudamapper_1_1Overlap.html#ab3594748a49ae4472ca28a03b05ddb7d">claragenomics::cudamapper::Overlap::num_residues_</a></div><div class="ttdeci">std::uint32_t num_residues_</div><div class="ttdoc">Number of residues (e.g anchors) between the two reads.</div><div class="ttdef"><b>Definition:</b> types.hpp:98</div></div>
<div class="ttc" id="astructclaragenomics_1_1cudamapper_1_1Overlap_html_a3d98a09e4ccd8bda66cb09a72adaf1fc"><div class="ttname"><a href="structclaragenomics_1_1cudamapper_1_1Overlap.html#a3d98a09e4ccd8bda66cb09a72adaf1fc">claragenomics::cudamapper::Overlap::query_read_id_</a></div><div class="ttdeci">read_id_t query_read_id_</div><div class="ttdoc">internal read ID for query</div><div class="ttdef"><b>Definition:</b> types.hpp:80</div></div>
<div class="ttc" id="astructclaragenomics_1_1cudamapper_1_1Anchor_html_a3c79e476eae0672a9a941e0980b6dcc3"><div class="ttname"><a href="structclaragenomics_1_1cudamapper_1_1Anchor.html#a3c79e476eae0672a9a941e0980b6dcc3">claragenomics::cudamapper::Anchor::query_read_id_</a></div><div class="ttdeci">read_id_t query_read_id_</div><div class="ttdoc">read ID of query</div><div class="ttdef"><b>Definition:</b> types.hpp:64</div></div>
<div class="ttc" id="astructclaragenomics_1_1cudamapper_1_1ArrayBlock_html_a3fca81e893b35e0648977b00f21b7e7e"><div class="ttname"><a href="structclaragenomics_1_1cudamapper_1_1ArrayBlock.html#a3fca81e893b35e0648977b00f21b7e7e">claragenomics::cudamapper::ArrayBlock::first_element_</a></div><div class="ttdeci">size_t first_element_</div><div class="ttdoc">index of the first element of the block</div><div class="ttdef"><b>Definition:</b> types.hpp:28</div></div>
<div class="ttc" id="astructclaragenomics_1_1cudamapper_1_1Overlap_html_a2da1b559c8e45c6bc48eda8b60e40c11"><div class="ttname"><a href="structclaragenomics_1_1cudamapper_1_1Overlap.html#a2da1b559c8e45c6bc48eda8b60e40c11">claragenomics::cudamapper::Overlap::target_length_</a></div><div class="ttdeci">std::uint32_t target_length_</div><div class="ttdoc">Length of target sequence.</div><div class="ttdef"><b>Definition:</b> types.hpp:102</div></div>
<div class="ttc" id="astructclaragenomics_1_1cudamapper_1_1ArrayBlock_html"><div class="ttname"><a href="structclaragenomics_1_1cudamapper_1_1ArrayBlock.html">claragenomics::cudamapper::ArrayBlock</a></div><div class="ttdef"><b>Definition:</b> types.hpp:25</div></div>
<div class="ttc" id="astructclaragenomics_1_1cudamapper_1_1Overlap_html_a20866810acf35523e87efcb66181a224"><div class="ttname"><a href="structclaragenomics_1_1cudamapper_1_1Overlap.html#a20866810acf35523e87efcb66181a224">claragenomics::cudamapper::Overlap::query_end_position_in_read_</a></div><div class="ttdeci">position_in_read_t query_end_position_in_read_</div><div class="ttdoc">end position in the query</div><div class="ttdef"><b>Definition:</b> types.hpp:88</div></div>
<div class="ttc" id="astructclaragenomics_1_1cudamapper_1_1Anchor_html"><div class="ttname"><a href="structclaragenomics_1_1cudamapper_1_1Anchor.html">claragenomics::cudamapper::Anchor</a></div><div class="ttdef"><b>Definition:</b> types.hpp:51</div></div>
<div class="ttc" id="astructclaragenomics_1_1cudamapper_1_1Overlap_html_ad4721b3555a83acb588c54dc369f7797"><div class="ttname"><a href="structclaragenomics_1_1cudamapper_1_1Overlap.html#ad4721b3555a83acb588c54dc369f7797">claragenomics::cudamapper::Overlap::target_end_position_in_read_</a></div><div class="ttdeci">position_in_read_t target_end_position_in_read_</div><div class="ttdoc">end position in the target</div><div class="ttdef"><b>Definition:</b> types.hpp:90</div></div>
<div class="ttc" id="astructclaragenomics_1_1cudamapper_1_1Overlap_html_aef98d06e839295136d197fee76feb95e"><div class="ttname"><a href="structclaragenomics_1_1cudamapper_1_1Overlap.html#aef98d06e839295136d197fee76feb95e">claragenomics::cudamapper::Overlap::query_start_position_in_read_</a></div><div class="ttdeci">position_in_read_t query_start_position_in_read_</div><div class="ttdoc">start position in the query</div><div class="ttdef"><b>Definition:</b> types.hpp:84</div></div>
<div class="ttc" id="astructclaragenomics_1_1cudamapper_1_1Overlap_html_a31d4f58b24a2e3fc57b5bca803827360"><div class="ttname"><a href="structclaragenomics_1_1cudamapper_1_1Overlap.html#a31d4f58b24a2e3fc57b5bca803827360">claragenomics::cudamapper::Overlap::overlap_complete</a></div><div class="ttdeci">bool overlap_complete</div><div class="ttdoc">Whether the overlap is considered valid by the generating overlapper.</div><div class="ttdef"><b>Definition:</b> types.hpp:104</div></div>
<div class="ttc" id="astructclaragenomics_1_1cudamapper_1_1Overlap_html_a03cb25f83ca6344ad1b4108c1d910f0c"><div class="ttname"><a href="structclaragenomics_1_1cudamapper_1_1Overlap.html#a03cb25f83ca6344ad1b4108c1d910f0c">claragenomics::cudamapper::Overlap::target_start_position_in_read_</a></div><div class="ttdeci">position_in_read_t target_start_position_in_read_</div><div class="ttdoc">start position in the target</div><div class="ttdef"><b>Definition:</b> types.hpp:86</div></div>
<div class="ttc" id="astructclaragenomics_1_1cudamapper_1_1Overlap_html_a6d01fc190b1cba1c6b41cd89d672b032"><div class="ttname"><a href="structclaragenomics_1_1cudamapper_1_1Overlap.html#a6d01fc190b1cba1c6b41cd89d672b032">claragenomics::cudamapper::Overlap::target_read_id_</a></div><div class="ttdeci">read_id_t target_read_id_</div><div class="ttdoc">internal read ID for target</div><div class="ttdef"><b>Definition:</b> types.hpp:82</div></div>
<div class="ttc" id="astructclaragenomics_1_1cudamapper_1_1Anchor_html_ad5e41665c86c77044b2ba2c939fdbb86"><div class="ttname"><a href="structclaragenomics_1_1cudamapper_1_1Anchor.html#ad5e41665c86c77044b2ba2c939fdbb86">claragenomics::cudamapper::Anchor::query_position_in_read_</a></div><div class="ttdeci">position_in_read_t query_position_in_read_</div><div class="ttdoc">position of first sketch element in query_read_id_</div><div class="ttdef"><b>Definition:</b> types.hpp:68</div></div>
<div class="ttc" id="astructclaragenomics_1_1cudamapper_1_1Anchor_html_af4dc10f114030a8e3a53f3bad3cd20b2"><div class="ttname"><a href="structclaragenomics_1_1cudamapper_1_1Anchor.html#af4dc10f114030a8e3a53f3bad3cd20b2">claragenomics::cudamapper::Anchor::Anchor</a></div><div class="ttdeci">Anchor()</div><div class="ttdoc">empty default constructor to prevent costly instantiations of all elements when initializing containe...</div><div class="ttdef"><b>Definition:</b> types.hpp:59</div></div>
<div class="ttc" id="astructclaragenomics_1_1cudamapper_1_1Anchor_html_ad58b2a619bd71c37c337ed44e45b4d23"><div class="ttname"><a href="structclaragenomics_1_1cudamapper_1_1Anchor.html#ad58b2a619bd71c37c337ed44e45b4d23">claragenomics::cudamapper::Anchor::target_position_in_read_</a></div><div class="ttdeci">position_in_read_t target_position_in_read_</div><div class="ttdoc">position of second sketch element in target_read_id_</div><div class="ttdef"><b>Definition:</b> types.hpp:70</div></div>
<div class="ttc" id="astructclaragenomics_1_1cudamapper_1_1ArrayBlock_html_a33ff27afee2ddb07e6fbdda0ff1de229"><div class="ttname"><a href="structclaragenomics_1_1cudamapper_1_1ArrayBlock.html#a33ff27afee2ddb07e6fbdda0ff1de229">claragenomics::cudamapper::ArrayBlock::block_size_</a></div><div class="ttdeci">std::uint32_t block_size_</div><div class="ttdoc">number of elements of the block</div><div class="ttdef"><b>Definition:</b> types.hpp:30</div></div>
<div class="ttc" id="astructclaragenomics_1_1cudamapper_1_1Overlap_html_a1c0b9bac9b2e15f70c60fcdae9728fd7"><div class="ttname"><a href="structclaragenomics_1_1cudamapper_1_1Overlap.html#a1c0b9bac9b2e15f70c60fcdae9728fd7">claragenomics::cudamapper::Overlap::relative_strand</a></div><div class="ttdeci">RelativeStrand relative_strand</div><div class="ttdoc">Relative strand: Forward (&quot;+&quot;) or Reverse(&quot;-&quot;)</div><div class="ttdef"><b>Definition:</b> types.hpp:96</div></div>
<div class="ttc" id="astructclaragenomics_1_1cudamapper_1_1Overlap_html_a7d37018aff3304bbe75b2d612b55c057"><div class="ttname"><a href="structclaragenomics_1_1cudamapper_1_1Overlap.html#a7d37018aff3304bbe75b2d612b55c057">claragenomics::cudamapper::Overlap::query_read_name_</a></div><div class="ttdeci">char * query_read_name_</div><div class="ttdoc">query read name (e.g from FASTA)</div><div class="ttdef"><b>Definition:</b> types.hpp:92</div></div>
<div class="ttc" id="astructclaragenomics_1_1cudamapper_1_1Overlap_html"><div class="ttname"><a href="structclaragenomics_1_1cudamapper_1_1Overlap.html">claragenomics::cudamapper::Overlap</a></div><div class="ttdef"><b>Definition:</b> types.hpp:77</div></div>
<div class="ttc" id="astructclaragenomics_1_1cudamapper_1_1Overlap_html_afcb7e39abf2761899ff1abb3c95b82ca"><div class="ttname"><a href="structclaragenomics_1_1cudamapper_1_1Overlap.html#afcb7e39abf2761899ff1abb3c95b82ca">claragenomics::cudamapper::Overlap::target_read_name_</a></div><div class="ttdeci">char * target_read_name_</div><div class="ttdoc">target read name (e.g from FASTA)</div><div class="ttdef"><b>Definition:</b> types.hpp:94</div></div>
<div class="ttc" id="astructclaragenomics_1_1cudamapper_1_1Anchor_html_ae9ae1af9e2feaea69ebde6b165966cec"><div class="ttname"><a href="structclaragenomics_1_1cudamapper_1_1Anchor.html#ae9ae1af9e2feaea69ebde6b165966cec">claragenomics::cudamapper::Anchor::target_read_id_</a></div><div class="ttdeci">read_id_t target_read_id_</div><div class="ttdoc">read ID of target</div><div class="ttdef"><b>Definition:</b> types.hpp:66</div></div>
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